Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/10404
Title: DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data
Authors: Takan, Savaş
Allmer, Jens
Keywords: Mass spectrometry
De novo sequencing
Ontology
DNMSO
DNML
Format
Issue Date: 2020
Publisher: PeerJ Inc.
Abstract: For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
Description: PubMed: 33150092
URI: https://doi.org/10.7717/peerj.10216
https://hdl.handle.net/11147/10404
ISSN: 2167-8359
Appears in Collections:PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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